Difference between revisions of "Annotation Conf. Call 2017-03-14"

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(Software, Infrastructure)
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== Software, Infrastructure ==
== Software, Infrastructure ==
*GO-Help, Ontology migration to github, Jenkins pipeline - Chris, Seth, Moni
*GO-Help, Ontology migration to github, Jenkins pipeline - Chris, Seth, Moni, Eric
** [https://drive.google.com/open?id=0B8kRPmmvPJU3S1Fwck9CTzNEUVE GO Consortium Meeting 2016 overview]
** https://github.com/geneontology/go-site/blob/master/metadata/datasets/
*Migration of annotation files to github at some point in the future?
*Migration of annotation files to github at some point in the future?

Revision as of 14:04, 13 March 2017

Bluejeans URL



GO Meeting Reminder

Software, Infrastructure

Annotation Review

  • Review of IMP annotations for possible use of new qualifiers
    • On the February 14th call, we discussed adding new qualifiers to describe the relationship between a gene/gene product and a GO BP term
    • Right now, the default relation between a gene/gene product and a GO BP term is 'involved in', but for a long time we've wanted a way to be more specific about describing this relation
    • Action item from February 14th call, was for groups to start looking at their existing BP annotations, specifically IMP, to determine whether the default involved in qualifier is still appropriate, and if not, how would they describe the relations between the gene/gene product and process?
    • BP_Annotation_Qualifiers_Spreadsheet
    • Are there general principles we can derive to help with applying qualifiers to new and existing legacy annotations?
      • Defining starts and ends of processes will be critical for doing this.
        • Signaling, or otherwise well-defined, molecular pathways vs BPs like behaviors or developmental processes
        • Look at genes annotated to both the process and regulation of the process
    • Explore effects on enrichment analyses - if we give users the option to filter annotations based on use of specific qualifiers, what might the outcome be?
    • David H has run gene sets from three papers using VLAD including and excluding IMP evidence codes.
    • GO and phenotype enrichment analyses may be complementary. Can/should we start encouraging users to do both?
  • Single-step biological processes - review annotations to help assess impact if such terms are obsoleted
    • Github ticket 'Remove all single-step BP classes'
    • What terms could possibly be considered single-step processes?
      • Look at MF-BP links
    • Mary D's analysis shows that there are 2380 bioentities that have experimental annotation to phosphorylation or its children that do not have annotation to kinase or its children. This is just one example.

Working Groups

  • Transcription factor decision tree
    • From Rachael: The update is that we have revised the decision tree, which is attached above (see github ticket), and we would like feedback on it from this working group. When the working group are happy with it, then we will announce it at a future annotation call and get it added to the website.
  • Annotating high throughput experiments
    • Proposed first meeting: Tuesday, March 21st, 8am PST